Multilayered horizontal operon transfers from bacteria reconstruct a thiamine salvage pathway in yeasts DOI Open Access
Carla Gonçalves, Paula Gonçalves

Proceedings of the National Academy of Sciences, Journal Year: 2019, Volume and Issue: 116(44), P. 22219 - 22228

Published: Oct. 14, 2019

Horizontal acquisition of bacterial genes is presently recognized as an important contribution to the adaptation and evolution eukaryotic genomes. However, mechanisms underlying expression consequent selection fixation prokaryotic in new setting are largely unknown. Here we show that composing pathway for synthesis essential vitamin B1 (thiamine) were lost ancestor a yeast lineage, Wickerhamiella/Starmerella (W/S) clade, known harbor unusually large number alien origin. The thiamine was subsequently reassembled, at least twice, by multiple HGT events from different donors involving both single entire operons. In W/S-clade species Starmerella bombicola obtained direct genetic evidence all functional. reconstructed composed operating coordinately scavenge derivatives environment. newly acquired operons involved repertoire until now only sparsely documented, namely longer intergenic regions, post-horizontal gene transfer (HGT) fusions fostering coordinated expression, relocation, possibly recombination generating mosaic genes. results provide additional occurred recurrently this lineage crucial reestablishment functions similar used across broad range microbes promote their

Language: Английский

Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum DOI Creative Commons
Xing‐Xing Shen, Dana A. Opulente, Jacek Kominek

et al.

Cell, Journal Year: 2018, Volume and Issue: 175(6), P. 1533 - 1545.e20

Published: Nov. 1, 2018

Language: Английский

Citations

532
HGT is widespread in insects and contributes to male courtship in lepidopterans DOI Creative Commons
Yang Li, Zhiguo Liu, Chao Liu

et al.

Cell, Journal Year: 2022, Volume and Issue: 185(16), P. 2975 - 2987.e10

Published: July 18, 2022

Horizontal gene transfer (HGT) is an important evolutionary force shaping prokaryotic and eukaryotic genomes. HGT-acquired genes have been sporadically reported in insects, a lineage containing >50% of animals. We systematically examined HGT 218 high-quality genomes diverse insects found that they acquired 1,410 exhibiting functions, including many not previously reported, via 741 distinct transfers from non-metazoan donors. Lepidopterans had the highest average number genes. introns exhibited substantially higher expression levels than lacking introns, suggesting intron gains were likely involved adaptation. Lastly, we used CRISPR-Cas9 system to edit prevalent unreported LOC105383139, which was transferred into last common ancestor moths butterflies. In diamondback moths, males LOC105383139 courted females significantly less. conclude has major contributor insect

Language: Английский

Citations

103
Genomic factors shape carbon and nitrogen metabolic niche breadth across Saccharomycotina yeasts DOI
Dana A. Opulente, Abigail L. LaBella, Marie‐Claire Harrison

et al.

Science, Journal Year: 2024, Volume and Issue: 384(6694)

Published: April 25, 2024

Organisms exhibit extensive variation in ecological niche breadth, from very narrow (specialists) to broad (generalists). Two general paradigms have been proposed explain this variation: (i) trade-offs between performance efficiency and breadth (ii) the joint influence of extrinsic (environmental) intrinsic (genomic) factors. We assembled genomic, metabolic, data nearly all known species ancient fungal subphylum Saccharomycotina (1154 yeast strains 1051 species), grown 24 different environmental conditions, examine evolution. found that large differences carbon utilization traits yeasts stem genes encoding specific metabolic pathways, but we limited evidence for trade-offs. These comprehensive argue factors shape microbes.

Language: Английский

Citations

38
Eukaryotic Acquisition of a Bacterial Operon DOI Creative Commons
Jacek Kominek, Drew T. Doering, Dana A. Opulente

et al.

Cell, Journal Year: 2019, Volume and Issue: 176(6), P. 1356 - 1366.e10

Published: Feb. 21, 2019

Language: Английский

Citations

89
From bumblebee to bioeconomy: Recent developments and perspectives for sophorolipid biosynthesis DOI
Sven Dierickx,

Martijn Castelein,

Jelle Remmery

et al.

Biotechnology Advances, Journal Year: 2021, Volume and Issue: 54, P. 107788 - 107788

Published: June 21, 2021

Language: Английский

Citations

67
Synergistic Effect Enhances Aromatic Profile in Beer Brewing Through Mixed-Culture Fermentation of Pichia kluyveri and Saccharomyces cerevisiae var. diastaticus DOI Creative Commons

Youyan Rong,

Xiaoxue Yu,

Kai Hong

et al.

Fermentation, Journal Year: 2025, Volume and Issue: 11(3), P. 148 - 148

Published: March 17, 2025

Saccharomyces cerevisiae is one of the important species traditional fermented foods and beverages. However, incorporating non-Saccharomyces in fermentation process a promising strategy to improve organoleptic profile. In this study, we assessed potential wild Pichia kluyveri strain (PKL) augment aromatic profile beer brewing while maintaining high attenuation through inoculation with var. diastaticus yeast (SY) both simultaneous (SI-PKL/SY) sequential (SE-3-PKL/SY) approaches. The performance was analyzed by residual sugar content, volatile organic compounds, sensory evaluation. results indicated that co-fermentation methods yielded levels comparable those SY monoculture fermentation. 2-phenethyl acetate, isoamyl linalool SE-3-PKL/SY increased 12.00, 12.37, 1.17 folds than monoculture, respectively. Furthermore, incremental concentrations these compounds contributed highest acceptability prominent fruity notes coculture. current study first report on brewing. These findings highlighted importance shaping ameliorative aroma production.

Language: Английский

Citations

1
Multi-Omics Driven Metabolic Network Reconstruction and Analysis of Lignocellulosic Carbon Utilization in Rhodosporidium toruloides DOI Creative Commons
Joonhoon Kim, Samuel T. Coradetti, Young‐Mo Kim

et al.

Frontiers in Bioengineering and Biotechnology, Journal Year: 2021, Volume and Issue: 8

Published: Jan. 8, 2021

An oleaginous yeast Rhodosporidium toruloides is a promising host for converting lignocellulosic biomass to bioproducts and biofuels. In this work, we performed multi-omics analysis of carbon utilization in R. reconstructed the genome-scale metabolic network . High-quality models model organisms orthologous protein mapping were used build draft reconstruction. The reconstruction was manually curated using functional annotation data including transcriptomics, proteomics, metabolomics, RB-TDNA sequencing. investigate metabolism lipid accumulation utilization. developed validated against high-throughput growth phenotyping gene fitness data, further refined resolve inconsistencies between prediction data. We believe that most complete accurate available date.

Language: Английский

Citations

46
Sophorolipids bioproduction in the yeast Starmerella bombicola: Current trends and perspectives DOI
Muneer Ahmed Qazi, Qinhong Wang, Zongjie Dai

et al.

Bioresource Technology, Journal Year: 2021, Volume and Issue: 346, P. 126593 - 126593

Published: Dec. 20, 2021

Language: Английский

Citations

43
Grape-associated fungal community patterns persist from berry to wine on a fine geographical scale DOI Creative Commons
Jonathan T. Martiniuk,

Jonah Hamilton,

T. L. Dodsworth

et al.

FEMS Yeast Research, Journal Year: 2023, Volume and Issue: 23

Published: Jan. 1, 2023

Abstract Wine grape fungal community composition is influenced by abiotic factors including geography and vintage. Compositional differences may correlate with different wine metabolite sensory profiles, suggesting a microbial role in the shaping of wine's terroir, or regional character. While wine-associated has been studied extensively at sub-regional scale, it not explored detail on fine geographical scales over multiple harvests. Over two years, we examined communities Vitis Vinifera cv. Pinot noir berry surfaces, crushed grapes, lab spontaneous fermentations from three vineyards within < 1 km radius Canada's Okanagan Valley region. We also evaluated effect winery environment exposure sampling grapes fermented commercial scale. Spatiotemporal structure was evident among surface, fermentation samples, each vineyard exhibiting distinct signature. Crushed populations were richer fermentative yeast species compared to surface populations. Our study suggests that, as level, contribute fine-scale -terroir,’ significant implications for single-vineyard wines.

Language: Английский

Citations

18
Genomic and ecological factors shaping specialism and generalism across an entire subphylum DOI Creative Commons
Dana A. Opulente, Abigail L. LaBella, Marie‐Claire Harrison

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: June 22, 2023

Organisms exhibit extensive variation in ecological niche breadth, from very narrow (specialists) to broad (generalists). Paradigms proposed explain this either invoke trade-offs between performance efficiency and breadth or underlying intrinsic extrinsic factors. We assembled genomic (1,154 yeast strains 1,049 species), metabolic (quantitative measures of growth 843 species 24 conditions), (environmental ontology 1,088 species) data nearly all known the ancient fungal subphylum Saccharomycotina examine evolution. found large interspecific differences carbon stem genes encoding specific pathways but no evidence a limited role These comprehensive argue that factors driving microbial variation.

Language: Английский

Citations

18